Additional:
When I try to use pin 5 or 6 for the A channel it does work.
But pin 9 or 10 won't do a thing.
Most certainly I am missing something small somewhere....
Found out what the problem is, when using the Servo Library, PWM is disabled on Pin 9 & 10.
I used both Tinkerkit servo connections on the Motor shield board which are/were on Pin 5 & 6.
So to get Yun I2C free (Pin 2 & 3), use both Motor shield PWM channels AND use both TK servo's:
Disable Brake A and Brake B on Motorshield (unavoidable consequence, at least Pin 9 in my case)
Rewire Motorshield Tinkerkit Out/Pin ~5 to Out/Pin ~9
Rewire Motorshield Tinkerkit Out/Pin ~6 to Out/Pin ~10
Rewire PWM Channel A Out/Pin ~3 to Out/Pin ~5
Weird that servo's still work on Pin 9 & 10 whilst PWM says to be disabled when using servo lib, but it works.
Maybe a userfriendly tip for Arduino: create a Yun version of the motor shield or jumpers or such.
I am not going to cut pins while another proto board comes on top, instead I am going to rewire the board itselve.
If the motor shield is the last/top board (also did this for testing) bending/cutting pins and use bread board wires to rewire works too!
P.s. Digital pin 0 and 1 also seem to be unusable as I/O, they interconnect/bridge Linux and ATmega32u4 .
Hope this helps for other people reading this post!